iirc, the 'pull request' is to the owner of the original repo (or other interested parties) informing them that you have mods (etc) for them to review - so I don't see any issues with your workflow so far
I use Atlassian SourceTree btw for git (its free !!!), since I'm visual in nature (as opposed to command-line, although there's another basic window based tool as well) - SourceTree has a Shift+Alt+P key combination for issuing a pull request
I think this is what you are referring to
http://git-scm.com/docs/git-request-pull[
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